WiP_STASH/tests/test.data.parameter.R
In MikeKSmith/MSToolkit: The MSToolkit Library For Clinical Trial Design
test_that("test.data.param.ext", {
testParamFile <- "testParam.csv"
otherFiles <- paste("testParam", c("nonmem", "spaceDelim",
"tabDelim"), sep = ".")
wrongTestParamFile <- "wrongTestParam.csv"
expect_error(createExternalParameters(-20), info = "`subjects` must be positive")
expect_error(createExternalParameters(20, names = ".54325,5432"),
info = "invalid `names`")
expect_error(createExternalParameters(20, names = "X,X"),
info = "duplicated `names`")
expect_error(createExternalParameters(20, names = "X,Y",
idCol = "X"), info = "duplicated names between `SUBJ` and `names`")
expect_error(createExternalParameters(20, names = "X", dataId = ".54325"),
info = "invalid `dataId`")
expect_error(createExternalParameters(20, names = "X", dataId = "ID,SUB"),
info = "`dataId` should be of length one")
expect_error(createExternalParameters(20, names = "X", idCol = ".54325"),
info = "invalid `idCol`")
expect_error(createExternalParameters(20, names = "X", idCol = "ID,SUB"),
info = "`idCol` should be of length one")
expect_error(createExternalParameters(20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B1"), info = "Duplicated values in betNames")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
file = "doesNotExists.csv", workingPath = parameters.datapath),
info = "File does not exist")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
file = wrongTestParamFile, workingPath = parameters.datapath),
info = "wrong formatted file")
expect_error(createExternalParameters(20, names = "X,Y,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath),
info = "missing variables in file")
expect_error(createExternalParameters(20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
idCol = "SUB"), info = "missing ID variables in file")
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "w"), info = "wrong errStruc")
dataNone <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2)
for (i in otherFiles) {
newData <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = i, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2)
expect_true(all(dim(dataNone) == dim(newData)), info = paste("Check correct dimensions when importing",
i))
expect_true(all(names(dataNone) == names(newData)), info = paste("Check correct column names when importing",
i))
expect_true(all(round(dataNone$ED50, 3) == newData$ED50),
info = paste("Check correct ED50 column when importing",
i))
expect_true(all(round(dataNone$B1, 3) == newData$B1),
info = paste("Check correct B1 column when importing",
i))
}
dataAdd <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Add", betNames = "B1,B2", seed = 2)
dataLogNorm <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Log", betNames = "B1,B2", seed = 2)
dataProp <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Pro", betNames = "B1,B2", seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
info = "Testing the Additive errStruc")
expect_true(identical(dataNone$ED50 + dataNone$B2, dataAdd$ED50),
info = "Testing the Additive errStruc")
expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
info = "Testing the Log-Normal errStruc")
expect_true(identical(dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50),
info = "Testing the Log-Normal errStruc")
expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
info = "Testing the Proportional errStruc")
expect_true(identical(dataNone$ED50 * (1 + dataNone$B2),
dataProp$ED50), info = "Testing the Proportional errStruc")
dataNone <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", seed = 2)
dataAdd <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "2,1",
seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B2, dataAdd$E0),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$ED50 + dataNone$B1, dataAdd$ED50),
info = "Testing the Additive errStruc and betNums")
dataNone <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataAdd <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataLogNorm <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "L", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataProp <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "P", betNames = "B1,B2", betNums = "1,3",
seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$ED50, dataAdd$ED50), info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$EMAX + dataNone$B2, dataAdd$EMAX),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
info = "Testing the Log-Normal errStruc and betNums")
expect_true(identical(dataNone$ED50, dataLogNorm$ED50), info = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
expect_true(identical(dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX),
info = "Testing the Log-Normal errStruc and betNums")
expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
info = "Testing the Proportional errStruc and betNums")
expect_true(identical(dataNone$ED50, dataProp$ED50), info = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
expect_true(identical(dataNone$EMAX * (1 + dataNone$B2),
dataProp$EMAX), info = "Testing the Proportional errStruc and betNums")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "f09-124"), info = "wrong refColName")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "REF"), info = "refColName not in the data")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "ID", refCol = "1,2,3"), info = "refColName not in the data")
testCovFile <- "testCovariates.csv"
importCov <- createExternalCovariates(20, names = "X1", dataId = "ID",
file = testCovFile, workingPath = covariates.datapath,
refCol = "ID")
refcolvalues <- importCov$ID.refCol
importPar <- createExternalParameters(20, names = "B1,B2",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "ID", refCol = refcolvalues)
iData <- read.csv(file.path(parameters.datapath, testParamFile))[,
c("ID", "B1", "B2")]
for (ref in refcolvalues) {
expect_true(all(iData[iData$ID == ref, "B1"][1] == importPar[refcolvalues ==
ref, "B1"]), info = "Testing the refCol system")
}
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "1"), info = "#betNames != #betNums")
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "a,b"), info = "wrong betNums format")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2"), info = "Need betNums if index mismatch")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "@fewf-+fw"), info = "Non sense code")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0 < EMAX < 1 "), info = "Too many comparators")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0"), info = "Too few comparators")
expect_true(all(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0")$E0 < 0), info = "test that the subset is applied correctly")
subData <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = c("E0 < 0", "1 <= B1 <= 2"))
expect_true(all(subData$E0 < 0), info = "test that the subset is applied correctly with multiple subsets")
expect_true(all(subData$B1 >= 1 & subData$B1 <= 2), info = "test that the subset is applied correctly with two comparators")
data1 <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
rnorm(2100) + runif(2)
data2 <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
expect_equal(data2, data1)
})
test_that("test.data.param.norm", {
expect_error(createNormalParameters(-50), info = "subjects should be positive")
expect_error(createNormalParameters(50, names = "X, Y", mean = "0,a"),
info = "wrong mean")
expect_error(createNormalParameters(50, names = "X,X", mean = "0,a"),
info = "duplicated names")
expect_error(createNormalParameters(50, names = "X,Y", mean = "0,0,0"),
info = "dimension problem")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1,0,0,-1,0,-1"), info = "wrong covariance matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1,0,0,1,0,1,2,3,4"), info = "wrong covariance matrix dims")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", maxDraws = -1), info = "wrong maxDraws value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", maxDraws = 5:6), info = "wrong maxDraws value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", digits = -1), info = "wrong digits value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", digits = 1:2), info = "wrong digits value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = ".45",
betCov = "1"), info = "wrong betNames value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "R",
betCov = "1"), info = "wrong betNames value, not a subset of names")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "-1"), info = "wrong betCov matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1,2,3"), info = "wrong betCov matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1", range = "]t43t534w-02354"), info = "non sense code")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1", range = "X"), info = "wrong range code, not enough comparators")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "N", seed = 99)
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 99)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "L", seed = 99)
errStrucDiff <- round(dataAdd[, c("X", "Y", "Z")] - (dataNone[,
c("X", "Y", "Z")] + dataNone[, paste(c("X", "Y", "Z"),
".Between", sep = "")]), 2)
expect_true(all(unlist(errStrucDiff == 0)), info = "checking the errStruc")
expect_true(all(dataLogNorm[, c("X", "Y", "Z")] - dataNone[,
c("X", "Y", "Z")] * exp(dataNone[, paste(c("X", "Y",
"Z"), ".Between", sep = "")] == 0)), info = "checking the errStruc with None and Log Normal")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "None", seed = 99, digits = 10)
dataNone$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "Add", seed = 99, digits = 10)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Log", seed = 99,
digits = 10)
.roundIt <- MSToolkit:::.roundIt
expect_true(identical(.roundIt(dataAdd[, c("X", "Y")], 5),
.roundIt(dataNone[, c("X", "Y")] + dataNone[, paste(c("X",
"Y"), ".Between", sep = "")], 5)), info = "check the errStruc, not all between, None and Add")
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z",
"Y"), ".Between", sep = "")])
expect_equal(v2, v1, info = "\ncheck the errStruc, not all between, None and Prop, different order(1)")
expect_true(identical(dataAdd$Z, dataNone$Z), info = "check the errStruc, not between, None and Add")
expect_true(identical(dataLogNorm$Z, dataNone$Z), info = "check the errStruc, not between, None and Prop")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "Z,Y", betCov = "1", betMean = "0,0",
errStruc = "N", seed = 99, digits = 5)
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "Z,Y", betCov = "1", betMean = "0,0",
errStruc = "A", seed = 99, digits = 5)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "L", seed = 99,
digits = 5)
expect_true(all(.roundIt(dataAdd[, c("Z", "Y")] - (dataNone[,
c("Z", "Y")] + dataNone[, paste(c("Z", "Y"), ".Between",
sep = "")]), 3) == 0), info = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z",
"Y"), ".Between", sep = "")])
expect_equal(v2, v1, info = "\ncheck the errStruc, not all between, None and Prop, different order(2)")
expect_true(all(dataAdd$X - dataNone$X == 0), info = "check the errStruc, not between, None and Prop, different order")
expect_true(all(dataLogNorm$X - dataNone$X == 0), info = "check the errStruc, not between, None and Prop, different order")
dataFixed <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1")
for (va in c("X", "Y", "Z")) {
expect_true(all(diff(dataFixed[[va]]) == 0), info = "check the fixed parameters")
}
})
test_that("test.data.param.wrap", {
testParamFile <- "testParam.csv"
wrongTestParamFile <- "wrongTestParam.csv"
expect_error(createParameters(-10), info = "wrong subject (negative)")
expect_error(createParameters(10, idCol = "ID, SUB"), info = "wrong id (too long)")
expect_error(createParameters(10, idCol = "08234ID"), info = "wrong id")
expect_error(createParameters(10, flagName = "PAROMIT, OMIT"),
info = "wrong flagName (too long)")
expect_error(createParameters(10, idCol = "082PAROMIT"),
info = "wrong flagName")
d1 <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 99)
d2 <- createParameters(50, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A", seed = 99)
expect_true(identical(d1, d2), info = "only normal")
d1 <- createExternalParameters(20, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath,
dataId = "ID", errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
d2 <- createParameters(20, extNames = "E0,ED50,EMAX", extDataId = "ID",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3",
seed = 81)
expect_true(identical(d1, d2), info = "only external")
dNor <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 81)
dExt <- createExternalParameters(50, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
dAll <- createParameters(50, extNames = "E0,ED50,EMAX", extFile = testParamFile,
workingPath = parameters.datapath, extErrStruc = "A",
extBetween = "B1,B2", extBetweenNums = "1,3", extDataId = "ID",
seed = 81, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A")
expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
dNor <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 81, range = "Y < 3")
dExt <- createExternalParameters(50, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath,
dataId = "ID", errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81, )
dAll <- createParameters(50, extNames = "E0,ED50,EMAX", extFile = testParamFile,
workingPath = parameters.datapath, extErrStruc = "A",
extBetween = "B1,B2", extBetweenNums = "1,3", extDataId = "ID",
seed = 81, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A", genRange = "Y < 3")
expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
expect_equal(dAll$PAROMIT, dNor$PAROMIT, info = "checking the PAROMIT")
})
test_that("test.parameter.rangeExclude", {
expect_error(createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", errStruc = "A", seed = 99, range = "Y < 50",
maxDraws = 1, parRangeTolerance = 0.9), info = "Bad range specified")
expect_true(is.data.frame(createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", errStruc = "A", seed = 99, range = "Y < 100",
maxDraws = 1, parRangeTolerance = 0.9)), info = "Good range specified")
warnData <- suppressWarnings(createNormalParameters(500,
names = "X,Y,Z", mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1", errStruc = "A", seed = 99,
range = "Y < 50", parRangeTolerance = 0.1, maxDraws = 1))
expect_true(is.data.frame(warnData) & any(warnData$PAROMIT ==
1), info = "Dataset returned with parameter omits")
})
test_that("test.parameter.sf3", {
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
info = "digits should be positive")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "N", digits = "2")
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "A", digits = "2")
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2")
expect_equal(round(dataAdd[, c("X", "Y", "Z")], 2), dataAdd[,
c("X", "Y", "Z")], info = "check the atomic digits (add)")
expect_equal(round(dataLogNorm[, c("X", "Y", "Z")], 2), dataLogNorm[,
c("X", "Y", "Z")], info = "check the atomic digits (prop)")
expect_equal(round(dataNone[, c("X", "Y", "Z", "X.Between",
"Y.Between")], 2), dataNone[, c("X", "Y", "Z", "X.Between",
"Y.Between")], info = "check the atomic digits (prop)")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "N", digits = "2,3,2")
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "A", digits = "2,3,2")
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2,3,2")
expect_equal(round(dataAdd$X, 2), dataAdd$X, info = "check the vector digits (add,X)")
expect_equal(round(dataAdd$Y, 3), dataAdd$Y, info = "check the vector digits (add,Y)")
expect_equal(round(dataAdd$Z, 2), dataAdd$Z, info = "check the vector digits (add,Y)")
expect_equal(round(dataLogNorm$X, 2), dataLogNorm$X, info = "check the vector digits (Prop,X)")
expect_equal(round(dataLogNorm$Y, 3), dataLogNorm$Y, info = "check the vector digits (Prop,Y)")
expect_equal(round(dataLogNorm$Z, 2), dataLogNorm$Z, info = "check the vector digits (Prop,Y)")
expect_equal(round(dataNone$X, 2), dataNone$X, info = "check the vector digits (None,X)")
expect_equal(round(dataNone$Y, 3), dataNone$Y, info = "check the vector digits (None,Y)")
expect_equal(round(dataNone$Z, 2), dataNone$Z, info = "check the vector digits (None,Y)")
expect_equal(round(dataNone$X.Between, 2), dataNone$X.Between,
info = "check the vector digits (None,X.Between)")
expect_equal(round(dataNone$Y.Between, 3), dataNone$Y.Between,
info = "check the vector digits (None,Y.Between)")
})
test_that("test.parameter.sf8", {
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
betNames = "X,Y", covariance = "1", betMean = "0,0",
errStruc = "N", seed = 99)
expect_true(all(dataNone[, c("X.Between", "Y.Between")] ==
0), info = "checking 0 covariance by default for between effects")
data.sf8 <- createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", seed = 99)
expect_true(all(sweep(data.sf8[, c("X", "Y", "Z")], 2, c(0,
50, 100), "-") == 0), info = "checking the 0 covariance by default")
})
MikeKSmith/MSToolkit documentation built on Feb. 15, 2024, 5:32 p.m.
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test_that("test.data.param.ext", {
testParamFile <- "testParam.csv"
otherFiles <- paste("testParam", c("nonmem", "spaceDelim",
"tabDelim"), sep = ".")
wrongTestParamFile <- "wrongTestParam.csv"
expect_error(createExternalParameters(-20), info = "`subjects` must be positive")
expect_error(createExternalParameters(20, names = ".54325,5432"),
info = "invalid `names`")
expect_error(createExternalParameters(20, names = "X,X"),
info = "duplicated `names`")
expect_error(createExternalParameters(20, names = "X,Y",
idCol = "X"), info = "duplicated names between `SUBJ` and `names`")
expect_error(createExternalParameters(20, names = "X", dataId = ".54325"),
info = "invalid `dataId`")
expect_error(createExternalParameters(20, names = "X", dataId = "ID,SUB"),
info = "`dataId` should be of length one")
expect_error(createExternalParameters(20, names = "X", idCol = ".54325"),
info = "invalid `idCol`")
expect_error(createExternalParameters(20, names = "X", idCol = "ID,SUB"),
info = "`idCol` should be of length one")
expect_error(createExternalParameters(20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B1"), info = "Duplicated values in betNames")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
file = "doesNotExists.csv", workingPath = parameters.datapath),
info = "File does not exist")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
file = wrongTestParamFile, workingPath = parameters.datapath),
info = "wrong formatted file")
expect_error(createExternalParameters(20, names = "X,Y,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath),
info = "missing variables in file")
expect_error(createExternalParameters(20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
idCol = "SUB"), info = "missing ID variables in file")
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "w"), info = "wrong errStruc")
dataNone <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2)
for (i in otherFiles) {
newData <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = i, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2)
expect_true(all(dim(dataNone) == dim(newData)), info = paste("Check correct dimensions when importing",
i))
expect_true(all(names(dataNone) == names(newData)), info = paste("Check correct column names when importing",
i))
expect_true(all(round(dataNone$ED50, 3) == newData$ED50),
info = paste("Check correct ED50 column when importing",
i))
expect_true(all(round(dataNone$B1, 3) == newData$B1),
info = paste("Check correct B1 column when importing",
i))
}
dataAdd <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Add", betNames = "B1,B2", seed = 2)
dataLogNorm <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Log", betNames = "B1,B2", seed = 2)
dataProp <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "Pro", betNames = "B1,B2", seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
info = "Testing the Additive errStruc")
expect_true(identical(dataNone$ED50 + dataNone$B2, dataAdd$ED50),
info = "Testing the Additive errStruc")
expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
info = "Testing the Log-Normal errStruc")
expect_true(identical(dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50),
info = "Testing the Log-Normal errStruc")
expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
info = "Testing the Proportional errStruc")
expect_true(identical(dataNone$ED50 * (1 + dataNone$B2),
dataProp$ED50), info = "Testing the Proportional errStruc")
dataNone <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", seed = 2)
dataAdd <- createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "2,1",
seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B2, dataAdd$E0),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$ED50 + dataNone$B1, dataAdd$ED50),
info = "Testing the Additive errStruc and betNums")
dataNone <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataAdd <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataLogNorm <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "L", betNames = "B1,B2", betNums = "1,3",
seed = 2)
dataProp <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "P", betNames = "B1,B2", betNums = "1,3",
seed = 2)
expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$ED50, dataAdd$ED50), info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$EMAX + dataNone$B2, dataAdd$EMAX),
info = "Testing the Additive errStruc and betNums")
expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
info = "Testing the Log-Normal errStruc and betNums")
expect_true(identical(dataNone$ED50, dataLogNorm$ED50), info = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
expect_true(identical(dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX),
info = "Testing the Log-Normal errStruc and betNums")
expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
info = "Testing the Proportional errStruc and betNums")
expect_true(identical(dataNone$ED50, dataProp$ED50), info = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
expect_true(identical(dataNone$EMAX * (1 + dataNone$B2),
dataProp$EMAX), info = "Testing the Proportional errStruc and betNums")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "f09-124"), info = "wrong refColName")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "REF"), info = "refColName not in the data")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "ID", refCol = "1,2,3"), info = "refColName not in the data")
testCovFile <- "testCovariates.csv"
importCov <- createExternalCovariates(20, names = "X1", dataId = "ID",
file = testCovFile, workingPath = covariates.datapath,
refCol = "ID")
refcolvalues <- importCov$ID.refCol
importPar <- createExternalParameters(20, names = "B1,B2",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
refColName = "ID", refCol = refcolvalues)
iData <- read.csv(file.path(parameters.datapath, testParamFile))[,
c("ID", "B1", "B2")]
for (ref in refcolvalues) {
expect_true(all(iData[iData$ID == ref, "B1"][1] == importPar[refcolvalues ==
ref, "B1"]), info = "Testing the refCol system")
}
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "1"), info = "#betNames != #betNums")
expect_error(createExternalParameters(20, names = "E0,ED50",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "a,b"), info = "wrong betNums format")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2"), info = "Need betNums if index mismatch")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "@fewf-+fw"), info = "Non sense code")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0 < EMAX < 1 "), info = "Too many comparators")
expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0"), info = "Too few comparators")
expect_true(all(createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0")$E0 < 0), info = "test that the subset is applied correctly")
subData <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
subset = c("E0 < 0", "1 <= B1 <= 2"))
expect_true(all(subData$E0 < 0), info = "test that the subset is applied correctly with multiple subsets")
expect_true(all(subData$B1 >= 1 & subData$B1 <= 2), info = "test that the subset is applied correctly with two comparators")
data1 <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
rnorm(2100) + runif(2)
data2 <- createExternalParameters(20, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
expect_equal(data2, data1)
})
test_that("test.data.param.norm", {
expect_error(createNormalParameters(-50), info = "subjects should be positive")
expect_error(createNormalParameters(50, names = "X, Y", mean = "0,a"),
info = "wrong mean")
expect_error(createNormalParameters(50, names = "X,X", mean = "0,a"),
info = "duplicated names")
expect_error(createNormalParameters(50, names = "X,Y", mean = "0,0,0"),
info = "dimension problem")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1,0,0,-1,0,-1"), info = "wrong covariance matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1,0,0,1,0,1,2,3,4"), info = "wrong covariance matrix dims")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", maxDraws = -1), info = "wrong maxDraws value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", maxDraws = 5:6), info = "wrong maxDraws value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", digits = -1), info = "wrong digits value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", digits = 1:2), info = "wrong digits value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = ".45",
betCov = "1"), info = "wrong betNames value")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "R",
betCov = "1"), info = "wrong betNames value, not a subset of names")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "-1"), info = "wrong betCov matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1,2,3"), info = "wrong betCov matrix")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1", range = "]t43t534w-02354"), info = "non sense code")
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betMean = "0", betNames = "X",
betCov = "1", range = "X"), info = "wrong range code, not enough comparators")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "N", seed = 99)
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 99)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "L", seed = 99)
errStrucDiff <- round(dataAdd[, c("X", "Y", "Z")] - (dataNone[,
c("X", "Y", "Z")] + dataNone[, paste(c("X", "Y", "Z"),
".Between", sep = "")]), 2)
expect_true(all(unlist(errStrucDiff == 0)), info = "checking the errStruc")
expect_true(all(dataLogNorm[, c("X", "Y", "Z")] - dataNone[,
c("X", "Y", "Z")] * exp(dataNone[, paste(c("X", "Y",
"Z"), ".Between", sep = "")] == 0)), info = "checking the errStruc with None and Log Normal")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "None", seed = 99, digits = 10)
dataNone$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "Add", seed = 99, digits = 10)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Log", seed = 99,
digits = 10)
.roundIt <- MSToolkit:::.roundIt
expect_true(identical(.roundIt(dataAdd[, c("X", "Y")], 5),
.roundIt(dataNone[, c("X", "Y")] + dataNone[, paste(c("X",
"Y"), ".Between", sep = "")], 5)), info = "check the errStruc, not all between, None and Add")
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z",
"Y"), ".Between", sep = "")])
expect_equal(v2, v1, info = "\ncheck the errStruc, not all between, None and Prop, different order(1)")
expect_true(identical(dataAdd$Z, dataNone$Z), info = "check the errStruc, not between, None and Add")
expect_true(identical(dataLogNorm$Z, dataNone$Z), info = "check the errStruc, not between, None and Prop")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "Z,Y", betCov = "1", betMean = "0,0",
errStruc = "N", seed = 99, digits = 5)
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
covariance = "1", betNames = "Z,Y", betCov = "1", betMean = "0,0",
errStruc = "A", seed = 99, digits = 5)
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "L", seed = 99,
digits = 5)
expect_true(all(.roundIt(dataAdd[, c("Z", "Y")] - (dataNone[,
c("Z", "Y")] + dataNone[, paste(c("Z", "Y"), ".Between",
sep = "")]), 3) == 0), info = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z",
"Y"), ".Between", sep = "")])
expect_equal(v2, v1, info = "\ncheck the errStruc, not all between, None and Prop, different order(2)")
expect_true(all(dataAdd$X - dataNone$X == 0), info = "check the errStruc, not between, None and Prop, different order")
expect_true(all(dataLogNorm$X - dataNone$X == 0), info = "check the errStruc, not between, None and Prop, different order")
dataFixed <- createNormalParameters(50, names = "X,Y,Z",
mean = "0,50,100", covariance = "1")
for (va in c("X", "Y", "Z")) {
expect_true(all(diff(dataFixed[[va]]) == 0), info = "check the fixed parameters")
}
})
test_that("test.data.param.wrap", {
testParamFile <- "testParam.csv"
wrongTestParamFile <- "wrongTestParam.csv"
expect_error(createParameters(-10), info = "wrong subject (negative)")
expect_error(createParameters(10, idCol = "ID, SUB"), info = "wrong id (too long)")
expect_error(createParameters(10, idCol = "08234ID"), info = "wrong id")
expect_error(createParameters(10, flagName = "PAROMIT, OMIT"),
info = "wrong flagName (too long)")
expect_error(createParameters(10, idCol = "082PAROMIT"),
info = "wrong flagName")
d1 <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 99)
d2 <- createParameters(50, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A", seed = 99)
expect_true(identical(d1, d2), info = "only normal")
d1 <- createExternalParameters(20, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath,
dataId = "ID", errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
d2 <- createParameters(20, extNames = "E0,ED50,EMAX", extDataId = "ID",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3",
seed = 81)
expect_true(identical(d1, d2), info = "only external")
dNor <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 81)
dExt <- createExternalParameters(50, names = "E0,ED50,EMAX",
dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81)
dAll <- createParameters(50, extNames = "E0,ED50,EMAX", extFile = testParamFile,
workingPath = parameters.datapath, extErrStruc = "A",
extBetween = "B1,B2", extBetweenNums = "1,3", extDataId = "ID",
seed = 81, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A")
expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
dNor <- createNormalParameters(50, names = "X,Y,Z", mean = "0,0,0",
covariance = "1", betNames = "X,Y,Z", betCov = "1", betMean = "0,0,0",
errStruc = "A", seed = 81, range = "Y < 3")
dExt <- createExternalParameters(50, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath,
dataId = "ID", errStruc = "A", betNames = "B1,B2", betNums = "1,3",
seed = 81, )
dAll <- createParameters(50, extNames = "E0,ED50,EMAX", extFile = testParamFile,
workingPath = parameters.datapath, extErrStruc = "A",
extBetween = "B1,B2", extBetweenNums = "1,3", extDataId = "ID",
seed = 81, genNames = "X,Y,Z", genFixedMean = "0,0,0",
genFixedCov = "1", genBetweenNames = "X,Y,Z", genBetweenCov = "1",
genBetweenMean = "0,0,0", genErrStruc = "A", genRange = "Y < 3")
expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
expect_equal(dAll$PAROMIT, dNor$PAROMIT, info = "checking the PAROMIT")
})
test_that("test.parameter.rangeExclude", {
expect_error(createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", errStruc = "A", seed = 99, range = "Y < 50",
maxDraws = 1, parRangeTolerance = 0.9), info = "Bad range specified")
expect_true(is.data.frame(createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", errStruc = "A", seed = 99, range = "Y < 100",
maxDraws = 1, parRangeTolerance = 0.9)), info = "Good range specified")
warnData <- suppressWarnings(createNormalParameters(500,
names = "X,Y,Z", mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1", errStruc = "A", seed = 99,
range = "Y < 50", parRangeTolerance = 0.1, maxDraws = 1))
expect_true(is.data.frame(warnData) & any(warnData$PAROMIT ==
1), info = "Dataset returned with parameter omits")
})
test_that("test.parameter.sf3", {
expect_error(createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
info = "digits should be positive")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "N", digits = "2")
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "A", digits = "2")
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2")
expect_equal(round(dataAdd[, c("X", "Y", "Z")], 2), dataAdd[,
c("X", "Y", "Z")], info = "check the atomic digits (add)")
expect_equal(round(dataLogNorm[, c("X", "Y", "Z")], 2), dataLogNorm[,
c("X", "Y", "Z")], info = "check the atomic digits (prop)")
expect_equal(round(dataNone[, c("X", "Y", "Z", "X.Between",
"Y.Between")], 2), dataNone[, c("X", "Y", "Z", "X.Between",
"Y.Between")], info = "check the atomic digits (prop)")
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "N", digits = "2,3,2")
dataAdd <- createNormalParameters(50, names = "X,Y,Z", mean = "100,100,100",
covariance = "1", betNames = "X,Y", betCov = "1", betMean = "0,0",
errStruc = "A", digits = "2,3,2")
dataLogNorm <- createNormalParameters(50, names = "X,Y,Z",
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2,3,2")
expect_equal(round(dataAdd$X, 2), dataAdd$X, info = "check the vector digits (add,X)")
expect_equal(round(dataAdd$Y, 3), dataAdd$Y, info = "check the vector digits (add,Y)")
expect_equal(round(dataAdd$Z, 2), dataAdd$Z, info = "check the vector digits (add,Y)")
expect_equal(round(dataLogNorm$X, 2), dataLogNorm$X, info = "check the vector digits (Prop,X)")
expect_equal(round(dataLogNorm$Y, 3), dataLogNorm$Y, info = "check the vector digits (Prop,Y)")
expect_equal(round(dataLogNorm$Z, 2), dataLogNorm$Z, info = "check the vector digits (Prop,Y)")
expect_equal(round(dataNone$X, 2), dataNone$X, info = "check the vector digits (None,X)")
expect_equal(round(dataNone$Y, 3), dataNone$Y, info = "check the vector digits (None,Y)")
expect_equal(round(dataNone$Z, 2), dataNone$Z, info = "check the vector digits (None,Y)")
expect_equal(round(dataNone$X.Between, 2), dataNone$X.Between,
info = "check the vector digits (None,X.Between)")
expect_equal(round(dataNone$Y.Between, 3), dataNone$Y.Between,
info = "check the vector digits (None,Y.Between)")
})
test_that("test.parameter.sf8", {
dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
betNames = "X,Y", covariance = "1", betMean = "0,0",
errStruc = "N", seed = 99)
expect_true(all(dataNone[, c("X.Between", "Y.Between")] ==
0), info = "checking 0 covariance by default for between effects")
data.sf8 <- createNormalParameters(500, names = "X,Y,Z",
mean = "0,50,100", seed = 99)
expect_true(all(sweep(data.sf8[, c("X", "Y", "Z")], 2, c(0,
50, 100), "-") == 0), info = "checking the 0 covariance by default")
})
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